Studies dealing with the structure and function of the type II IAP elements were continued. These elements can be distinguished from the more abundant type I IAP elements by a specific 270 bp insertion designated AIIins. Sequencing of several type II IAP elements revealed that part of the region coding for retroviral endonuclease is duplicated and has made it possible to isolate and clone sequences containing only AIIins for use as a specific probe for these elements. Using this probe to analyze Southern blots of mouse genomic DNA, we have shown that: (a) association with other repetitive sequences appears to be a general property of many typeII IAP elements; (b) amplification of type IIB elements in MOPC-315 myeloma is 6-fold and in MOPC-104E myeloma 2-fold relative to embryo DNA; (c) partial demethylation of type II elements in myeloma cells correlates with the known transcriptional activity of the element subclasses. We propose that association with L1 repeats is a feature of transcriptionally silent type II IAP elements, and may reflect their location in a particular chromosomal environment. In situ hybidization of this probe to mouse metaphase chromosomes revealed that the type II elements are clustered on a limited number of chromosomes.